[gmx-users] problem with gromcas 4.5.3

leila separdar separdar.leila at gmail.com
Sun Feb 27 10:20:39 CET 2011


I have installed gromacs version 4.5.3. when I want to use pdb2gmx for
generating .top and .gro files for 1000 argon atoms, in topology file I have
seen another atom O with mass 1.48594e-41 as below I do not know what to
do.I do not confront with such problems when I had 4.0.7 version of gromacs.
please help me. also I have used gromos43a1 force feild.
[ moleculetype ]
; Name            nrexcl
Other_chain_A       3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
; residue   1 GAS rtp GAS  q  0.0
     1         AR      1    GAS     AR      1          0          1   ; qtot
0
; residue   2 GAS rtp GAS  q  0.0
     2          O      2    GAS     AR      2          0 1.48594e-41   ;
qtot 0
; residue   3 GAS rtp GAS  q  0.0
     3          O      3    GAS     AR      3          0 1.48594e-41   ;
qtot 0
; residue   4 GAS rtp GAS  q  0.0
     4          O      4    GAS     AR      4          0 1.48594e-41   ;
qtot 0
; residue   5 GAS rtp GAS  q  0.0
     5          O      5    GAS     AR      5          0 1.48594e-41   ;
qtot 0
; residue   6 GAS rtp GAS  q  0.0
     6          O      6    GAS     AR      6          0 1.48594e-41   ;
qtot 0
; residue   7 GAS rtp GAS  q  0.0
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